Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus.

The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.

Evolution and multiple origins of zona pellucida genes in vertebrates.

Animal egg coats are composed of different glycoproteins collectively named zona pellucida (ZP) proteins. The characterized vertebrate genes encoding ZP proteins have been classified into six subfamilies, and exhibit low similarity to the ZP genes characterized in certain invertebrates. The origin and evolution of the vertebrate ZP genes remain obscure. A search against 97 representative metazoan species revealed various numbers (ranging from three to 33) of different putative egg-coat ZP genes in all 47 vertebrates and several ZP genes in five invertebrate species, but no putative ZP gene was found in the other 45 species. Based on phylogenetic and synteny analyses, all vertebrate egg-coat ZP genes were classified into eight ZP gene subfamilies. Lineage- and species-specific gene duplications and gene losses occurred frequently and represented the main causes of the patchy distribution of the eight ZP gene subfamilies in vertebrates. Thorough phylogenetic analyses revealed that the vertebrate ZP genes could be traced to three independent origins but were not orthologues of the characterized invertebrate ZP genes. Our results suggested that vertebrate egg-coat ZP genes should be classified into eight subfamilies, and a putative evolutionary map is proposed. These findings would aid the functional and evolutionary analyses of these reproductive genes in vertebrates.

Pathological and microbiological findings from mortality of the Chinese giant salamander (Andrias davidianus).

The Chinese giant salamander, Andrias davidianus, is a nationally protected and cultured species in China. Recently, a severe epizootic occurred in cultured Chinese giant salamanders in Hubei, Hunan, Sichuan, Shaanxi, and Zhejiang provinces of China, causing substantial economic losses. The typical clinical signs of diseased larval animals were jaw and abdominal swelling and subcutaneous hemorrhaging. Diseased adult animals exhibited skin hemorrhages, ulceration of the hind limbs, and multiple hemorrhagic spots in the visceral organs. Histopathological observation indicated tissue necrosis and cytoplasmic inclusions in the spleen, liver and kidney, suggestive of viral disease. A viral agent was isolated from affected tissues in cell culture. The virus was determined to be pathogenic after experimental infection. Electron microscopy revealed iridovirus-like virions with a size of 140-180 nm in diameter inside the kidney of naturally infected animals and in cell culture. The major capsid protein (MCP) of the virus exhibited 98-99 % sequence identity to ranaviruses. Additionally, phylogenetic analysis indicated that the virus belonged to the genus Ranavirus. Comparative analysis of the MCP gene sequence with those of other viruses previously isolated from Chinese giant salamanders revealed that these isolates were highly similar, although a few variations were observed. The virus was preliminarily named Chinese giant salamander iridovirus (GSIV).